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Commit a524547a authored by Amandine  PERRIN's avatar Amandine PERRIN
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publish singularity image for version 1.0

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Pipeline #36748 passed
"""PanACoTA""" """PanACoTA"""
__version__ = 20190425 __version__ = 1.0
...@@ -14,10 +14,6 @@ From:python:3.7-stretch ...@@ -14,10 +14,6 @@ From:python:3.7-stretch
# Install packages needed # Install packages needed
apt-get install -y wget apt-get install -y wget
# apt-get install -y \
# wget \
# python3 \
# python3-pip
# Upgrade pip # Upgrade pip
pip3 install --upgrade pip pip3 install --upgrade pip
...@@ -25,14 +21,6 @@ From:python:3.7-stretch ...@@ -25,14 +21,6 @@ From:python:3.7-stretch
# For manually-installed programs # For manually-installed programs
mkdir -p /opt/src mkdir -p /opt/src
# Update makeblastdb and blastp for prokka
cd /opt/src
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz && \
tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
rm ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install mash # Install mash
cd /opt/src cd /opt/src
wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\ wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
...@@ -40,7 +28,14 @@ From:python:3.7-stretch ...@@ -40,7 +28,14 @@ From:python:3.7-stretch
rm mash-Linux64-v2.2.tar &&\ rm mash-Linux64-v2.2.tar &&\
mv /opt/src/mash-Linux64-v2.2/mash /usr/local/bin &&\ mv /opt/src/mash-Linux64-v2.2/mash /usr/local/bin &&\
rm -r mash-Linux64-v2.2 rm -r mash-Linux64-v2.2
# Update makeblastdb and blastp for prokka
cd /opt/src
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.1+-x64-linux.tar.gz && \
tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
cp /opt/src/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
rm ncbi-blast-2.10.1+-x64-linux.tar.gz
# Install barrnap # Install barrnap
cd /opt/src cd /opt/src
...@@ -73,7 +68,6 @@ From:python:3.7-stretch ...@@ -73,7 +68,6 @@ From:python:3.7-stretch
/opt/src/prokka/bin/prokka --setupdb &&\ /opt/src/prokka/bin/prokka --setupdb &&\
ln -s /opt/src/prokka/bin/prokka /usr/local/bin ln -s /opt/src/prokka/bin/prokka /usr/local/bin
# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e # Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
cd /opt/src cd /opt/src
wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\ wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
...@@ -141,7 +135,6 @@ From:python:3.7-stretch ...@@ -141,7 +135,6 @@ From:python:3.7-stretch
cd /opt/src cd /opt/src
git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git git clone https://gitlab.pasteur.fr/aperrin/pipeline_annotation.git
cd /opt/src/pipeline_annotation cd /opt/src/pipeline_annotation
git checkout dev &&\
./make ./make
......
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